Personally I like to go out for time lapse right during rush hour for capturing headlights & tail lights for the obvious reasons of great light streams. However, I try and get out around 3am to 4am for the ultimate privacy. Only problem with this time of night, as in any city is that you run into is the type of people that are typically up at this hour. Trust me it's not typically other photo geeks trying to score a shot. My advice is if you need to shoot in places that are not that secure and your set up with your camera on your sticks, that you bring a large cardboard box that you can fold and unfold. It's great for blocking your expensive camera gear from prying eyes and you can step back from a safe distance and monitor your capture. Also remember that you don't always need to have your tripod extended all the way. Being lower to the ground (if the shot is able) keeps you a little more undercover.
If your shooting say from rooftops or such (which I highly recommend) this is 99% better for security and image composition quality (subject depending).
What are you shooting mostly? I can offer up some more tips if I know what you're trying to capture.